- BBClist - maillist.psb.ugent.be

Lecture Series in "Translational Bioinformatics and Systems Biomedicine".
by Francisco Azuaje 02 Jun '17

02 Jun '17

Dear Colleagues, This year in Luxembourg ?we begin hosting a Lecture Series in "Translational Bioinformatics and Systems Biomedicine" . Full provisional program is now available at:?? https://files.lih.lu/events/2017/Overview%20translational%20bioinformatics_… Our first lecture (on 19 June) will be given by Prof. Luonan Chen (Director of the Key Laboratory of Systems Biology @ Shanghai Institutes for Biological Sciences): http://tinyurl.com/y95k3bgv? Sincerely, Francisco. _________________________________ Francisco Azuaje, PhD Principal Investigator Proteome and Genome Research Unit Department of Oncology Luxembourg Institute of Health 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg Tel: +352 26970-875 Fax: +352 26970-719 Email: francisco.azuaje(a)lih.lu<mailto:francisco.azuaje@lih.lu> Website: https://www.lih.lu/ [http://files.lih.lu/outlookSignature/lih.jpg] Join us on Facebook and follow our activities on Twitter: https://www.facebook.com/Luxembourg.Institute.of.Health http://twitter.com/LIH_Luxembourg This message (including any attachments) is intended for the addressee only and may contain confidential and/or privileged information and/or information protected by intellectual property rights. If you have received this message by mistake, please notify the sender by return e-mail and delete this message from your system. You should not use, alter, copy or distribute this message or disclose its contents to anyone. E-mail transmission can not be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. Luxembourg Institute of Health shall not be responsible nor liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system.

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[Gtpb] Reproducible and Open Data Science - a hands-on course
by Pedro L. Fernandes 01 Jun '17

01 Jun '17

ANNOUNCEMENT/REMINDER RODS17 Reproducible and Open Data Science with Rutger Vos and Pedro Fernandes (Instructors) The above referenced hands-on training course is open for applications IMPORTANT DATES for this Course Deadline for applications: June 16th, 2017 <=== Course date: June 21st - 23rd 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Description: In an age of increasingly complex and data-intensive, collaborative scientific practices, scandals of irreproducibility, and a growing societal ethos of transparency and accountability, a new paradigm has arisen: Open Science. In this three day course, we will introduce to you the three organizing principles and practices that under-gird this paradigm: Open Access scholarly publishing Open Source software development Open Data integration and sharing For this, we will be introducing a set of technologies and ways of using them. The reasonable expectation is that the participants will feel empowered and start using them for the above purposes in a highly productive way. The use-cases that we will be working on are going to be based on bioinformatics, but the principles are very broadly applicable to other fields. You do not need to have any particular programming or otherwise computational experience beyond what is normally required from a scientist in graduate school and beyond, i.e., you should not be afraid of interacting with a computer and editing simple text files. http://gtpb.igc.gulbenkian.pt/bicourses/RODS17/ Hoping that this course meets your interests, Pedro Fernandes -- Pedro Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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BioSB Course Quantitative and Predictive Modelling, 26-30 June 2017 in Wageningen
by Celia van Gelder 30 May '17

30 May '17

BioSB Course Quantitative and Predictive Modelling Date: 26-30 June, 2017 Location: Wageningen Course Coordinators: Natal van Riel (TUE) & Jaap Molenaar (WUR) Website: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Registration: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Please note that this course is free of charge for PhDs who are or become a <http://biosb.nl/about/members/biosb-membership-information/> member of the BioSB research school. Description On June 26-30 2017, BioSB organises the second edition of the course Quantitative and Predictive Modelling (QPM). In this course the participants learn how to describe the dynamic behaviour of biological systems and to integrate experimental data. Concepts of modelling in terms of differential equations are introduced via a great variety of case studies taken from diverse practices. The course offers a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. The emphasis is on providing an introduction into modelling approaches rather than an in-depth treatment of a few techniques and aims as such at a broad audience. The course is a mixture of theory sessions and computer practicals. During the practicals most of the time Matlab will be used. Participants not acquainted with Matlab will get an introduction. The course has to be completed with assignments in the form of practical exercises as homework afterwards. Target audience and learning objectives This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences, Bioinformatics, Systems Biology or Biomedical Engineering. Participants from the private sector are also welcome. Participants are expected to have some experience in modelling with differential equations. The students will be provided with a theoretical basis, a variety of methods and a computational hands-on experience to handle differential equation modelling, parameter estimation and uncertainty analysis. In the course the students will learn: · How to set-up a dynamic model to represent biological networks using different interaction mechanisms · To implement, simulate and analyse dynamic network models in different software tools · To understand the common ground and the differences for applications in metabolic, regulatory, signalling, population and multi-scale biological processes · To integrate experimental data in modelling, estimate model parameters and assess the accuracy of parameter estimates and model predictions This course is part of the <http://biosb.nl/education/course-portfolio-2/> Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl <http://www.biosb.nl/> . Beste regards, Femke Francissen Femke Francissen Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: <mailto:femke.francissen@biosb.nl> femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl <http://www.biosb.nl/> LinkedIn <http://nl.linkedin.com/in/femkefrancissen> link <http://www.dtls.nl/wp-content/uploads/2014/09/BioSB_logo_full_250x226.jpg>

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C-COMEND: free Training in Translational research, BCRT Oct 9-13th, 2017, Berlin
by Celia van Gelder 30 May '17

30 May '17

Dear all, Please spread the announcement below as you see fit. Best Celia Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht This is to inform you that <https://www.helmholtz-hzi.de/de/aktuelles/veranstaltungen/c_comend/overview…> registration for the next free C-COMEND course is still open. The EU project C-COMEND offers PhD and Postdocs the opportunity to join a course on “Translational Research and Development“ in Berlin from 9th-13th of October 2017. The course consists of an introductory e‑learning (~ 24 hours student investment time) followed by a 5-day face-to-face workshop with speakers from Industry and Academia, including Bob Harris, Professor Immunotherapy, Karolinska Matthias Gottwald, Head of R&D Policy & Networking, BAYER Keith Williams, Director, KW Drug Developments Mike Hardman, former Vice President IMI Collaborations, AstraZeneca Mohamed Abou-El-Enein, Head of Clinical Development Platform, BCRT Participation is free of charge but participants will have to cover their travel costs. Deadline for <https://www.helmholtz-hzi.de/de/aktuelles/veranstaltungen/c_comend/overview/> application is June, 1st. It would be fantastic if you could support us by spreading this information to your colleagues, students and/ or other people in your network that might be interested, either by sharing this email (see also the attached flyer and preliminary program) or via <https://twitter.com/RebeccaLudwig2/status/862210038508773376> twitter, or <https://www.linkedin.com/feed/update/urn:li:activity:6262188458727604224/> LinkedIn and <https://www.facebook.com/photo.php?fbid=1113513968755159&set=gm.12572624210…> facebook. Thank you very much in advance for your time and effort! With kind regards, Rosan Vegter, DVM, PhD C-Comend Training Project Manager cid:image001.png@01D2D928.60139120 EATRIS | European infrastructure for translational medicine rosanvegter(a)eatris.eu | +31 (0)6 15 52 29 34 De Boelelaan 1118 | Room PK 4X 176 1081 HZ Amsterdam | The Netherlands +31 (0)20 4442254 | www.eatris.eu Working days: Monday, Tuesday, Friday <https://twitter.com/EatrisEric> Follow us on Twitter <http://translationalmedicine2017.eu/> cid:image002.png@01D2D928.60139120

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Cytoscape Advanced Tutorial @ ISMB this year
by P. Molenaar 19 May '17

19 May '17

Dear fellow researcher, At ISMB this year, the Cytoscape development team will be staging an all new advanced Cytoscape tutorial. It will be held the afternoon of Friday July 21 at the ISMB site in Prague. This tutorial is especially interesting given the fact that Cytoscape is being transformed as part of a Cytoscape Cyber Infrastructure and will support a full blown REST Api. You can sign up for it on the ISMB web site: https://www.iscb.org/ismbeccb2017-registration (note: the early bird registration ends the 15th of June) The full information is here: https://www.iscb.org/ismbeccb2017-program/tutorials#p4 The brief version is below. Hope to see you there! The Cytoscape development team Network Analysis in Cytoscape: Advanced Topics Intended audience The Advanced Topics tutorial is intended for an audience that has prior experience with at least one of the following: * Cytoscape software * Data integration and analytical methods * Network biology concepts * Bioinformatics analysis pipelines Goals, objectives and motivations By the end of tutorial, you should be able to: * Know when and how to use Cytoscape in your research area * Identify and discriminate relevant source of interactions, networks and datasets * Command programmatic control over Cytoscape * Integrate Cytoscape into your bioinformatics pipelines * Publish, share and export networks online * Generalize network analysis methods to multiple problem domains ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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Fwd: help me to find a good bioinformatician
by Stephane Rombauts 18 May '17

18 May '17

> From: "Walter Sanseverino" <wsanseverino(a)sequentiabiotech.com> > Sent: Wednesday, May 17, 2017 5:02:54 PM > Subject: help me to find a good bioinformatician > Hi guys, > I hope to find you well. > Please help me, we are looking a talented young bioinformatician. > thank you > Walter > Walter Sanseverino, PhD > Executive Director, Sequentia Biotech > Parc Cientific de Barcelona > Torre R 02A6/A7 > c/ Baldiri Reixac 4-8 > 08028 Barcelona > +34930107368 > [ http://www.sequentiabiotech.com/ | www.sequentiabiotech.com ] > LinkedIn: Follow Sequentia [ > https://www.linkedin.com/company/3068832?trk=tyah&trkInfo=tarId:14116362001… > | here ] > This message is intended exclusively for its addressee and may contain > information considered CONFIDENTIAL and protected by professional privilege. If > you are not the intended recipient you are hereby notified that any > dissemination, copy or disclosure of this communication is strictly prohibited > by law. If this message has been mistakenly received, please immediately notify > us via e-mail and delete it. > La información contenida en la presente transmisión es confidencial y su uso > únicamente está permitido a su(s) destinatario(s). Si Ud. no es la persona > destinataria de la presente transmisión, rogamos nos lo comunique de manera > inmediata por teléfono +34 935636600 y destruya cualquier copia de la misma > (tanto digitales como en papel). De conformidad con la Ley 15/99 Sequentia > Biotech S.L. le informa que los datos personales que facilite serán > incorporados a ficheros del que somos responsables y destinatarios y que tienen > por finalidad mantener las relaciones con Vd. Puede ejercer sus derechos de > acceso, rectificación, cancelación y oposición por e-mail [ > mailto:info@esario.com | info(a)sequentiabiotech.com ] incluyendo la palabra > PROTECCIÓN DE DATOS en el cuerpo del mensaje o bien en las dependencias sitas > en nuestras oficinas.

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BioSB Course Quantitative and Predictive Modelling, 26-30 June 2017 in Wageningen
by Femke Francissen 15 May '17

15 May '17

BioSB Course Quantitative and Predictive Modelling Date: 26-30 June, 2017 Location: Wageningen Course Coordinators: Natal van Riel (TUE) & Jaap Molenaar (WUR) Website: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Registration: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Please note that this course is free of charge for PhDs who are or become a member of the BioSB research school <http://biosb.nl/about/members/biosb-membership-information/>. Description On June 26-30 2017, BioSB organises the second edition of the course Quantitative and Predictive Modelling (QPM). In this course the participants learn how to describe the dynamic behaviour of biological systems and to integrate experimental data. Concepts of modelling in terms of differential equations are introduced via a great variety of case studies taken from diverse practices. The course offers a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. The emphasis is on providing an introduction into modelling approaches rather than an in-depth treatment of a few techniques and aims as such at a broad audience. The course is a mixture of theory sessions and computer practicals. During the practicals most of the time Matlab will be used. Participants not acquainted with Matlab will get an introduction. The course has to be completed with assignments in the form of practical exercises as homework afterwards. Target audience and learning objectives This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences, Bioinformatics, Systems Biology or Biomedical Engineering. Participants from the private sector are also welcome. Participants are expected to have some experience in modelling with differential equations. The students will be provided with a theoretical basis, a variety of methods and a computational hands-on experience to handle differential equation modelling, parameter estimation and uncertainty analysis. In the course the students will learn: - How to set-up a dynamic model to represent biological networks using different interaction mechanisms - To implement, simulate and analyse dynamic network models in different software tools - To understand the common ground and the differences for applications in metabolic, regulatory, signalling, population and multi-scale biological processes - To integrate experimental data in modelling, estimate model parameters and assess the accuracy of parameter estimates and model predictions This course is part of the Education Programme of BioSB <http://biosb.nl/education/course-portfolio-2/>, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl. Beste regards, Femke Francissen ** ** *Femke Francissen* Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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Workshop GATK Best Practices for Variant Discovery, 17-19 July 2017 - Registration open (second announcement)
by Bert Overduin 15 May '17

15 May '17

Dear all, I am happy to announce that for the third year in a row we have been able to get three members of the GATK team of the Broad Institute ( https://software.broadinstitute.org/gatk/) over to Edinburgh for a few days to teach a workshop on GATK Best Practices for Variant Discovery. Details of the workshop can be found below. With kind regards, Bert ********** GATK BEST PRACTICES FOR VARIANT DISCOVERY DATE: Monday 17 - Wednesday 19 July 2017 VENUE: The King's Buildings,The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 3 July 2017 CANCELLATION DEADLINE: Monday 10 July 2017 PLACES: 85 (lectures), 30 (hands-on sessions) (first come, first served) REGISTRATION FEE: £70 for the lectures, £35 for each half-day hands-on session (includes coffee/tea, but no lunch) INFORMATION: Bert Overduin (bert.overduin(a)ed.ac.uk) TO REGISTER: http://genomics.ed.ac.uk/services/gatk-best- practices-variant-discovery This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq-specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery, and we demonstrate the use of pipelining tools to assemble and execute GATK workflows. "Excellent opportunity to learn from world-renowned experts!" (April 2016) INSTRUCTORS GATK staff (The Broad Institute, Cambridge, MA, United States) WORKSHOP FORMAT The workshop is composed of one day of lectures (including many opportunities for Q&A) and two optional days of hands-on training, structured as follows: Lectures (day 1): Rationale, theory and application of the GATK Best Practices for Variant Discovery in high-throughput sequencing data. Hands-on 1 (day 2 am): Germline variant discovery (SNPs + Indels) Hands-on 2 (day 2 pm): Germline variant filtering (SNPs + Indels) Hands-on 3 (day 3 am): Somatic variant discovery (SNPs + Indels + CNV) Hands-on 4 (day 3 pm): Pipelining on the cloud with WDL Please note that the lectures part is mandatory. It is not possible to attend any of the hands-on sessions without attending the lectures. In the three optional hands-on sessions focused on analysis, we walk attendees through exercises that teach them how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to common use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK and Picard tools, dealing with problems, and using third-party tools such as Samtools, IGV, RStudio and RTG Tools. In the optional hands-on session on pipelining, we walk attendees through exercises that teach them to write workflow scripts using WDL, the Broad's new Workflow Description Language, and to execute these workflows locally as well as through publicly available cloud-based services. Please note that this workshop is focused on human data analysis. The majority of the materials presented applies equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points. WHO SHOULD ATTEND The lecture-based component of the workshop is aimed at a mixed audience of people who are new to the topic of variant discovery or to GATK, seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. Attendees should already be familiar with the basic terms and concepts of genetics and genomics. The hands-on component is aimed at novice to intermediate users who are seeking detailed guidance with GATK and related tools. Basic familiarity with the command line environment is required. Please note that for the hands-on sessions attendees will be expected to bring their own laptops with software preinstalled (detailed instructions will be posted two weeks before the workshop). Supported systems are Mac and Unix/Linux systems. MS Windows is not supported. COVERED TOPICS Lectures Introduction to variant discovery analysis and GATK Best Practices Marking Duplicates Indel Realignment Base Recalibration Variant Calling and Joint Genotyping Filtering variants with VQSR Genotype Refinement Workflow Callset Evaluation Somatic variant discovery with MuTect2 Preview of CNV discovery with GATK4 Hands-on 1 Germline variant discovery (SNPs + Indels) Hands-on 2 Germline variant filtering (SNPs + Indels) Hands-on 3 Somatic variant discovery (SNPs + Indels + CNV) Hands-on 4 Pipelining on the cloud with WDL -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Researcher meeting on the Dutch "National Plan Open Science"
by Egon Willighagen 13 May '17

13 May '17

(as indicated below, the meeting is aimed at *Dutch* researchers, but I believe it is relevant for the other BBC countries to be aware of the meeting.) During the its EU presidency last year, the Dutch government pushed to further Open Science as a European level. This has led to various activities, and at a local level in a "National Plan Open Science" (https://www.openscience.nl/) to enact the European "Amsterdam Call for Action on Open Science" (see [0]). On May 29, this National Plan will be discussed directly with researchers for the first time at a national meeting aimed at Dutch scientists. Besides some top down information with speakers like Sander Dekker (government) and Wim van den Doel (NWO), the meeting will be by researchers and for researchers: https://www.openscience.nl/nationaal-plan For example, during the lunch break researchers can present their own Open Science work or shop around and see how others are using Open Science in their research. This is organized as a Knowledge Commons session. After this 1.5h Open Science galore, there will be break out sessions where you can learn about various themes and discuss the issues you are facing. Mind you, this is the time to let the Dutch government hear your researcher voice and needs! Importantly, the meeting is for anyone doing research, whether at a university, a HBO, an institute, but even at home as a citizen scientist. After all, it's about Open Science and our European future. Also, it's not only about natural sciences, but also linguistics, humanities, social sciences, law, etc. With kind regards, Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/u/egonwillighagen

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RSG Student Symposium 2017 - Gent
by Daniele Parisi 10 May '17

10 May '17

RSG Belgium, the network that connects PhD students and young postdocs working in Bioinformatics, is proud to announce their 2017 Bioinformatics Symposium. Date: THURSDAY 8TH JUNE Abstract submission deadline: 31th MAY Place: GHENT UNIVERSITY, scientific park Keynote Speaker: YVES VAN DE PEER http://bioinformatics.psb.ugent.be/pe.../profile/yvesvandepeer [1] The RSG STUDENT SYMPOSIUM will be an half day of PRESENTATIONS, DISCUSSION AND NETWORKING from and for PhD students in Bioinformatics. The goal of this symposium is to give PhD students and young postdocs the opportunity to present their research as well as broaden their network. Please SUBSCRIBE AND SUBMIT YOUR ABSTRACT HERE, BEFORE MAY 31TH: https://docs.google.com/forms/d/e/1FAIpQLScjrKKk7DXi_aQv5E1PUCOt5bDw5gyLada… [2] You can also FIND US ON FACEBOOK: https://www.facebook.com/RSGBelgium/ [3] A NETWORK DINNER in the centre of the city follows the symposium (soon more information) -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Board member of PhD Leuven society Kasteelpark Arenberg 10 - box 2446 3001 Leuven, Belgium Tel: +32488794394 Links: ------ [1] https://l.facebook.com/l.php?u=http%3A%2F%2Fbioinformatics.psb.ugent.be%2Fp… [2] https://docs.google.com/forms/d/e/1FAIpQLScjrKKk7DXi_aQv5E1PUCOt5bDw5gyLada… [3] https://www.facebook.com/RSGBelgium/

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